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Thompson CC, Tschoeke D, Coutinho FH, Leomil L, Garcia GD, Otsuki K, Turcq BJ, Moreira LS, Turcq PFM, Cordeiro RC, Asp NE, Thompson FL. Diversity of Microbiomes Across a 13,000-Year-Old Amazon Sediment. MICROBIAL ECOLOGY 2023; 86:2202-2209. [PMID: 37017718 DOI: 10.1007/s00248-023-02202-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 02/23/2023] [Indexed: 06/19/2023]
Abstract
The microbiome is fundamental for understanding bacterial activities in sediments. However, only a limited number of studies have addressed the microbial diversity of Amazonian sediments. Here, we studied the microbiome of sediments from a 13,000-year BP core retrieved in a floodplain lake in Amazonia using metagenomics and biogeochemistry. Our aim was to evaluate the possible environmental influence over a river to a lake transition using a core sample. To this end, we sampled a core in the Airo Lake, a floodplain lake in the Negro River basin. The Negro River is the largest tributary of the Amazon River. The obtained core was divided into three strata: (i) surface, almost complete separation of the Airo Lake from the Negro River when the environment becomes more lentic with greater deposition of organic matter (black-colored sediment); (ii) transitional environment (reddish brown); and (iii) deep, environment with a tendency for greater past influence of the Negro River (brown color). The deepest sample possibly had the greatest influence of the Negro River as it represented the bottom of this river in the past, while the surface sample is the current Airo Lake bottom. In total, six metagenomes were obtained from the three different depth strata (total number of reads: 10.560.701; sequence length: 538 ± 24, mean ± standard deviation). The older (deeper) sediment strata contained a higher abundance of Burkholderia, Chitinophaga, Mucilaginibacter, and Geobacter, which represented ~ 25% of the metagenomic sequences. On the other hand, the more recent sediment strata had mainly Thermococcus, Termophilum, Sulfolobus, Archaeoglobus, and Methanosarcina (in total 11% of the metagenomic sequences). The sequence data were binned into metagenome-assembled genomes (MAGs). The majority of the obtained MAGs (n = 16) corresponded to unknown taxa, suggesting they may belong to new species. The older strata sediment microbiome was enriched with sulfur cycle genes, TCA cycle, YgfZ, and ATP-dependent proteolysis in bacteria. Meanwhile, serine-glyoxylate cycle, stress response genes, bacterial cell division, cell division-ribosomal stress protein cluster, and oxidative stress increased in the younger strata. Metal resistance and antimicrobial resistance genes were found across the entire core, including genes coding for fluoroquinolones, polymyxin, vancomycin, and multidrug resistance transporters. These findings depict the possible microbial diversity during the depositional past events and provided clues of the past microbial metabolism throughout time.
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Affiliation(s)
- Cristiane C Thompson
- Institute of Biology, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
| | - Diogo Tschoeke
- Institute of Biology, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Biomedical Engineer Program, COPPE (UFRJ), Rio de Janeiro, Brazil
| | - Felipe H Coutinho
- Institute of Biology, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Institut de Ciències del Mar (ICM-CSIC), Barcelona, Spain
| | - Luciana Leomil
- Institute of Biology, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Gizele D Garcia
- Institute of Biology, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
- Instituto de Ciências Médicas, Centro Multidisciplinar UFRJ Macae, Universidade Federal do Rio de Janeiro (UFRJ), RJ, Macae, Brazil
| | - Koko Otsuki
- Institute of Biology, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil
| | - Bruno J Turcq
- Institute de Recherche pour Le Dévelopment-Sorbonne, Université (UPMC, CNRS, IRD, MNHN) LOCEAN - Centre IRD France Nord, Bondy, France
| | - Luciane S Moreira
- Programa de Geoquímica, Universidade Federal Fluminense (UFF), Niterói, Rio de Janeiro, Brazil
| | - Patrícia F M Turcq
- Institute de Recherche pour Le Dévelopment-Sorbonne, Université (UPMC, CNRS, IRD, MNHN) LOCEAN - Centre IRD France Nord, Bondy, France
| | - Renato C Cordeiro
- Programa de Geoquímica, Universidade Federal Fluminense (UFF), Niterói, Rio de Janeiro, Brazil
| | - Nils E Asp
- Instituto de Estudos Costeiros (IECOS), Universidade Federal do Pará (UFPA), Bragança, Brazil
| | - Fabiano L Thompson
- Institute of Biology, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, Brazil.
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Oren A, Garrity GM. CANDIDATUS LIST No. 3. Lists of names of prokaryotic Candidatus taxa. Int J Syst Evol Microbiol 2022; 72. [PMID: 35100104 DOI: 10.1099/ijsem.0.005186] [Citation(s) in RCA: 251] [Impact Index Per Article: 125.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Aharon Oren
- The Institute of Life Sciences, The Hebrew University of Jerusalem, The Edmond J. Safra Campus, 9190401 Jerusalem, Israel
| | - George M Garrity
- Department of Microbiology & Molecular Genetics, Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824-4320, USA
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Flieder M, Buongiorno J, Herbold CW, Hausmann B, Rattei T, Lloyd KG, Loy A, Wasmund K. Novel taxa of Acidobacteriota implicated in seafloor sulfur cycling. THE ISME JOURNAL 2021; 15:3159-3180. [PMID: 33981000 PMCID: PMC8528874 DOI: 10.1038/s41396-021-00992-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2020] [Revised: 04/05/2021] [Accepted: 04/15/2021] [Indexed: 02/03/2023]
Abstract
Acidobacteriota are widespread and often abundant in marine sediments, yet their metabolic and ecological properties are poorly understood. Here, we examined metabolisms and distributions of Acidobacteriota in marine sediments of Svalbard by functional predictions from metagenome-assembled genomes (MAGs), amplicon sequencing of 16S rRNA and dissimilatory sulfite reductase (dsrB) genes and transcripts, and gene expression analyses of tetrathionate-amended microcosms. Acidobacteriota were the second most abundant dsrB-harboring (averaging 13%) phylum after Desulfobacterota in Svalbard sediments, and represented 4% of dsrB transcripts on average. Meta-analysis of dsrAB datasets also showed Acidobacteriota dsrAB sequences are prominent in marine sediments worldwide, averaging 15% of all sequences analysed, and represent most of the previously unclassified dsrAB in marine sediments. We propose two new Acidobacteriota genera, Candidatus Sulfomarinibacter (class Thermoanaerobaculia, "subdivision 23") and Ca. Polarisedimenticola ("subdivision 22"), with distinct genetic properties that may explain their distributions in biogeochemically distinct sediments. Ca. Sulfomarinibacter encode flexible respiratory routes, with potential for oxygen, nitrous oxide, metal-oxide, tetrathionate, sulfur and sulfite/sulfate respiration, and possibly sulfur disproportionation. Potential nutrients and energy include cellulose, proteins, cyanophycin, hydrogen, and acetate. A Ca. Polarisedimenticola MAG encodes various enzymes to degrade proteins, and to reduce oxygen, nitrate, sulfur/polysulfide and metal-oxides. 16S rRNA gene and transcript profiling of Svalbard sediments showed Ca. Sulfomarinibacter members were relatively abundant and transcriptionally active in sulfidic fjord sediments, while Ca. Polarisedimenticola members were more relatively abundant in metal-rich fjord sediments. Overall, we reveal various physiological features of uncultured marine Acidobacteriota that indicate fundamental roles in seafloor biogeochemical cycling.
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Affiliation(s)
- Mathias Flieder
- grid.10420.370000 0001 2286 1424Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Joy Buongiorno
- grid.411461.70000 0001 2315 1184Department of Microbiology, University of Tennessee, Knoxville, TN USA ,grid.421147.50000 0000 8528 5498Present Address: Division of Natural Sciences, Maryville College, Maryville, TN USA
| | - Craig W. Herbold
- grid.10420.370000 0001 2286 1424Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Bela Hausmann
- grid.10420.370000 0001 2286 1424Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria ,grid.10420.370000 0001 2286 1424Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria ,grid.22937.3d0000 0000 9259 8492Department of Laboratory Medicine, Medical University of Vienna, Vienna, Austria
| | - Thomas Rattei
- grid.10420.370000 0001 2286 1424Division of Computational Systems Biology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | - Karen G. Lloyd
- grid.411461.70000 0001 2315 1184Department of Microbiology, University of Tennessee, Knoxville, TN USA
| | - Alexander Loy
- grid.10420.370000 0001 2286 1424Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria ,grid.10420.370000 0001 2286 1424Joint Microbiome Facility of the Medical University of Vienna and the University of Vienna, Vienna, Austria ,grid.465498.2Austrian Polar Research Institute, Vienna, Austria
| | - Kenneth Wasmund
- grid.10420.370000 0001 2286 1424Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria ,grid.465498.2Austrian Polar Research Institute, Vienna, Austria ,grid.5117.20000 0001 0742 471XCenter for Microbial Communities, Department of Chemistry and Bioscience, Aalborg University, Aalborg, Denmark
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Medina-de la Rosa G, García-Oliva F, Alpuche-Solís ÁG, Ovando-Vázquez C, López-Lozano NE. The nutrient-improvement bacteria selected by Agave lechuguilla T. and their role in the rhizosphere community. FEMS Microbiol Ecol 2021; 97:6380485. [PMID: 34601598 DOI: 10.1093/femsec/fiab137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 09/27/2021] [Indexed: 11/14/2022] Open
Abstract
Agave lechuguilla has one of the widest distributions among other agave species in the Chihuahuan Desert. Their capacity to grow in poorly developed soils and harsh conditions has been related to their association with plant growth-promoting rhizobacteria. In this work, we explored how soil properties and plant growth stage influence the composition of the rhizobacterial communities, their interactions, and the enzymatic activity and abundance of nitrogen-fixing bacteria and organic phosphorus-mineralizing bacteria in two subregions of the Chihuahuan Desert. We found that mature plants of lechuguilla stimulated the activity and abundance of nutrient-improvement rhizobacteria, and these soil samples had a higher content of total organic carbon, ammonium (NH4) and nitrite + nitrate (NO2+NO3). Nutrient availability seems to be an essential driver of the bacterial community's structure since the genera with more connections (hubs) were those with known mechanisms related to the availability of nutrients, such as env. OPS17 (Bacteroidetes), Gemmatimonadaceae uncultured, S0134terrestrial group, BD211terrestrial group (Gemmatimonadetes), Chthoniobacteracea and Candidatus Udaeobacter (Verrucomicrobia). This work shows that the late growth stages of lechuguilla recruit beneficial bacteria that favor its establishment and tolerance to harsh conditions of the arid lands.
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Affiliation(s)
- Guadalupe Medina-de la Rosa
- CONACyT- Division de Ciencias Ambientales, Instituto Potosino de Investigación Científica y Tecnológica, A.C., 78216 San Luis Potosi, S.L.P., Mexico
| | - Felipe García-Oliva
- Instituto de Investigaciones en Ecosistemas y Sustentabilidad, Universidad Nacional Autónoma de México, 58190 Morelia, Mich., Mexico
| | - Ángel G Alpuche-Solís
- Division de Biologia Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., 78216 San Luis Potosi, S.L.P., Mexico
| | - Cesaré Ovando-Vázquez
- Division de Biologia Molecular, Instituto Potosino de Investigación Científica y Tecnológica, A.C., 78216 San Luis Potosi, S.L.P., Mexico.,CONACyT-Centro Nacional de Supercómputo, Instituto Potosino de Investigación Científica y Tecnológica, A.C., 78216 San Luis Potosi, S.L.P., Mexico
| | - Nguyen E López-Lozano
- CONACyT- Division de Ciencias Ambientales, Instituto Potosino de Investigación Científica y Tecnológica, A.C., 78216 San Luis Potosi, S.L.P., Mexico
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